The report can be filled out online under Leader and Clerk Resources (LCR) on LDS.org (clerk.lds.org or leader.lds.org or on your Tools menu on LDS.org), on the Reports menu.

(NOTE: I think the link aebrown gave to Record-Keeping and Technology Support (RKATS) for the Quarterly Report is broken, temporarily or permanently...at least for me it returns a page that says "The content on this page is restricted to certain roles. LDS Account sign-in is required." The same link returns the same message on LDS.org/lcr under Quarterly Report when you select "more" for more help documentation. I would assume that my role as an assistant stake clerk-membership would allow me to see that page on quarterly reports!)

If you also can't see that page, and until somone can get that fixed... Clerks can go to LDS.org/lcr and select Quarterly Report under the Reports tab. The Mouse-over help tips probably will give you enough help as you mouse over each item on the report. The Report can be submitted (after the first day of each new quarter) via MLS (until it goes away) or on LDS.org. You fill in the blank spots! The Blank report is printed from MLS...